User profiles for Hsuan-lin Her

Hsuan-lin Her

Graduate Student at UC San Diego
Verified email at ucsd.edu
Cited by 224

[PDF][PDF] Proteomic discovery of chemical probes that perturb protein complexes in human cells

…, JR Remsberg, MG Jaeger, K Rothamel, H Her… - Molecular Cell, 2023 - cell.com
Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule
binding assays have been introduced to address this problem. How compounds …

Remodeling oncogenic transcriptomes by small molecules targeting NONO

SG Kathman, SJ Koo, GL Lindsey, HL Her… - Nature chemical …, 2023 - nature.com
Much of the human proteome is involved in mRNA homeostasis, but most RNA-binding
proteins lack chemical probes. Here we identify electrophilic small molecules that rapidly and …

A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains

HL Her, YW Wu - Bioinformatics, 2018 - academic.oup.com
Motivation Antimicrobial resistance (AMR) is becoming a huge problem in both developed
and developing countries, and identifying strains resistant or susceptible to certain antibiotics …

[HTML][HTML] Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP

DA Lorenz, HL Her, KA Shen, K Rothamel, KR Hutt… - Nature …, 2023 - nature.com
… RBPs are color-coded with their annotated binding feature. Rows are labeled by their respective
… To determine the top targets for SLBP we first ranked all peaks by their P value and then …

[PDF][PDF] Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites

EA Boyle, HL Her, JR Mueller, JT Naritomi, GG Nguyen… - Cell Genomics, 2023 - cell.com
Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq)
has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To …

[HTML][HTML] Inferring a spatial code of cell-cell interactions across a whole animal body

…, I Shamie, J Chan, HL Her… - PLoS computational …, 2022 - journals.plos.org
Cell-cell interactions shape cellular function and ultimately organismal phenotype.
Interacting cells can sense their mutual distance using combinations of ligand-receptor pairs, …

[HTML][HTML] Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion

…, M Jain, LA Street, AT Tankka, D Schafer, HL Her… - Nature …, 2024 - nature.com
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform
expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion…

[HTML][HTML] PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains

HL Her, PT Lin, YW Wu - BMC bioinformatics, 2021 - Springer
Background Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is
becoming more and more important to accurately and swiftly identify AMR pathogenic strains. …

Using time-frequency features to recognize abnormal heart sounds

H Her, HW Chiu - 2016 Computing in Cardiology Conference …, 2016 - ieeexplore.ieee.org
Disease of the heart accounts for 6% of all death. Heart sound is a routine in physical examination
clinically, and is sensitive in detecting a subset of heart diseases. In the current study, …

Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites

HL Her, E Boyle, GW Yeo - Bioinformatics Advances, 2022 - academic.oup.com
Motivation Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding
sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often …